Updating iBooks

According to this article (http://support.apple.com/kb/HT5477) and this one (http://support.apple.com/kb/HT5558), whenever you update an iBook via iBooks Author, the bookmarks and highlights should migrate to the new file. Is this feature only supported on books that are distributed through the iBooks Store, or will it work for files that are distributed via a private enterprise system?

I have written a series of textbooks that are distributed privately and want to make sure that when I add content and update the files, the sales reps will still have their existing highlights, note cards and bookmarks. I tested it on my iPad and instead of updating the existing book (which was created in a previous version of iBooks Author), it added a new book to my bookshelf.